you PROBABLY still have the debug watch window displaying tc_test0_module.hw->COUNT16

the way that ASF seems to define peripherals with multiple "modes" has a different data structure for each mode "high up" in the structure, even if most of the registers are essentially parallel. But when you finally get to COUNT.reg, it will be only 16 bits instead of 32. (well, this explains the debug window only showing 16bits. What's the indication in your code that it's only using 16 bits?)